Bursting with Activity

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The heart gets all the glory in poetry and aphorisms, but it is the liver that plays a truly central role in orchestrating the entire body’s metabolism. In carrying out its many and varied tasks, the liver faces the tremendous challenge of constantly adjusting to changing conditions – for instance, keeping blood glucose at a steady level despite large mealtime fluctuations in the glucose supply. Weizmann Institute scientists have now revealed that genes in the liver operate in bursts rather than continuously – a pattern that may help optimize their activity, assisting the liver in coping with ongoing challenges. An in-depth understanding of this mechanism may shed new light on the way the liver, and perhaps other organs too, function in health and disease.
 
A similar mechanism had been earlier known to exist in bacteria: When it comes to bacterial genes, the initial stage of activity, the production of a messenger molecule called mRNA, often proceeds in bursts that vary randomly in length, resulting in widely varying mRNA levels in different bacterial cells. This pattern suggests a strategy that has been described as “bet-hedging”: The diversity in mRNA production ensures the survival of at least some of the bacteria, i.e., the ones for which mRNA levels happen to be best suited to the current circumstances.   
Dr. Shalev Itzkovitz
 
In the new study, reported in Molecular Cell, scientists led by Dr. Shalev Itzkovitz of the Molecular Cell Biology Department set out to explore the question: Do genes in the mammalian body resort to the same mechanism; that is, do they produce mRNA in bursts? The scientists used an innovative method developed in Itzkovitz’s lab that has, for the first time, made it possible to visualize individual mRNA molecules as they are being manufactured in intact mammalian tissue. The method combines advanced microscopy with computational approaches.   
 
Using this method, they showed that, just as in bacteria, genes in mouse liver tissue work in random bursts of varying length. The lifetimes of different mRNA molecules, it turns out, also vary; the mRNAs of some genes are longer-lasting than others. The combination of these two variables renders the control of liver gene activity extremely flexible. Thus an mRNA of a particular gene can be generated in long bursts; but if this mRNA itself is short-lived, stopping the bursts will rapidly put an end to the gene’s activity.
 
 
Activity of a glucose-manufacturing gene in mouse liver tissue, viewed under a fluorescence microscope. A high concentration of mRNA (red dots) reveals that this activity is highest near a blood vessel (PP) that bathes the tissue in oxygen-rich blood, essential for glucose manufacture
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
This flexibility can be crucial in performing the liver’s dynamic functions – for example, in regulating blood glucose. As part of ongoing maintenance, the liver takes up extra glucose when its levels are too high, then gradually releases it or synthesizes new glucose when levels drop. As glucose levels rise within minutes after a meal, the synthesis of new glucose must be able to stop instantly. The short-lived mRNA, which quickly disappears from the cell once gene activity is shut down, is perfectly suited to this end.
 
Indeed, the Weizmann study found that the mRNAs of two genes essential for glucose production are extremely short-lived. To compensate for their brief life span, they are produced in longer than average bursts, presumably to reduce the variability among cells caused by the bursts. On the other hand, other mRNAs, with a longer life span, are produced in shorter bursts.
Fluorescence microscope image of mouse liver cells. Cell membranes are in green; the cell nuclei (blue) contain different numbers of DNA strands, from the usual 2 to as many as 8
 
The scientists believe the bursty expression of genes could have evolved because it can protect the DNA from damage: Genes are physically more exposed when active, so by being active only at intervals, rather than permanently, they are less vulnerable to surrounding toxins. This feature is particularly important in an organ like the liver, which is involved in filtering out harmful substances.
 
The scientists also believe that the bursty activity may help explain a baffling feature of many liver cells: the presence of multiple copies of the genome, comprising four or eight DNA strands instead of the usual two. Their proposed explanation goes as follows: The bursts cause mRNA levels to fluctuate at random, but thanks to the extra DNA copies, each of which produces mRNA, this randomness is averaged out among cells. As a result, different liver cells end up producing a particular mRNA in a uniform manner. Indeed, in a “factory” such as the liver, where cells work together towards a common physiological goal, excessive variability among cells caused by such bursts could have been a disadvantage. 
 
Fluorescence microscope snapshots of mouse liver tissue revealing new mRNA, an indicator of gene activity (bright dots marked by white triangles). The lone new mRNA (left) indicates that its gene operates only in infrequent bursts; in contrast, the presence of numerous new mRNAs (right) suggests gene activity that proceeds in long, frequent bursts
 
 
The team that performed this research included Dr. Keren Bahar Halpern, Sivan Tanami, Shanie Landen, Michal Chapal, Liran Szlak, Anat Hutzler and Anna Nizhberg. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
Further clarification of the bursty gene expression in the liver may help reveal such mechanisms of faulty liver function as defective glucose metabolism, which leads to diabetes. The scientists have also found indications that bursty gene expression may be found in organs other than the liver, a finding that opens new ways of investigating the control of gene activity in different tissues.
 
 
 
 
Activity of a glucose-manufacturing gene in mouse liver tissue, viewed under a fluorescence microscope. A high concentration of mRNA (red dots) reveals that this activity is highest near a blood vessel (PP) that bathes the tissue in oxygen-rich blood, essential for glucose manufacture
Life Sciences
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Cells with an Edge

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Within the pancreas are little spherical structures called islets of Langerhans – a name that might conjure up images of cells lazing on a remote beach, sipping tropical drinks. That picture could not be further from the truth: The so-called beta cells, the major component of these islets, are some of the busiest, most connected cells in our bodies. They do sip, but it is the sugar in our bloodstream they taste; they then secrete insulin back into the bloodstream to regulate the metabolism of that sugar. And, according to new Weizmann Institute research, these cells submit to a very tight organization. The study, which appeared in Cell Reports, revealed, for the first time, an image of beta cells that are “edgy.” The details of how beta cells are shaped may change our understanding of how they function and lead to new insights into how glucose is regulated in the body.

 

Mouse islet of Langerhans; insulin-containing vesicles within beta cells are shown in white
 
Beta cells are those affected by diabetes: In type 1 diabetes they are attacked by an autoimmune response in the body, and in type 2 diabetes the body cells do not respond to the insulin they secrete, which eventually leads to their dysfunction. The beta cells are a minority in the pancreas, but the island-like arrangement within the “sea” of pancreatic cells enables them to function as an organ within an organ. A closer look at the arrangement of cells in an islet of Langerhans shows that they assemble in “rosette” patterns around veins running through the pancreas, with small arteries encircling the rosettes.
 
Prof. Ben-Zion Shilo, research student Erez Geron and Dr. Eyal Schejter of the Molecular Genetics Department wanted to zoom in a bit closer – to the molecular arrangements of these cells. Many had assumed that the cells were polar – that they concentrate some functions on one side and others on the opposite side. Polarity, according to this view, would enable the beta cell to compartmentalize its activities, possibly sensing on one side and secreting on the other. In addition, beta cells are related to other polar cells – for example, those that line the intestine. But no one had actually managed to observe clear hallmarks of polarity in beta cells.  

To investigate, Geron studied proteins on the cells’ outer membranes – where sensing and secretion take place. Isolating individual islets of Langerhans from a mouse pancreas, he inserted a fluorescent protein into several of their cells. The team then devised a technique that allowed them to visualize filamentous actin, a major component of the cellular cytoskeleton, just within a few individual cells of each islet, thus providing good contrast right at the cells’ contours. Since islets of Langerhans can be kept alive in the lab dish, the researchers were able to observe the shapes of beta cells at work.
 
 

                                                           Cell design on a line

Prof. Ben-Zion Shilo
 
What they saw surprised them: Rather than a polar arrangement, the actin in the membrane formed stiff, linear edges, like those on a cube, along the length of the cell, giving it the appearance of an angular tent with poles. But these lines were more than just support poles: Numerous thin protrusions extended from the cell along these lines, and membrane features congregated along them – signaling proteins, channels for letting in glucose, others for trading short messages encoded in calcium ions with neighboring cells, and even outlets for secreting insulin.

Why do these particular cells reject their polar heritage and go for edgy shapes? Why would they take all of their functions – sensing glucose, releasing insulin and intercellular communication – and align them together along these cell edges? Shilo says that they do not yet have all the answers, but he and his group have some definite clues. For example, they think that keeping the sensing and secreting machinery close together could increase efficiency and/or cut down on response time.

Further research will be needed to understand the exact function of the edges, but Shilo says the study points to an important role in cell-to-cell communication. Indeed, one of the major implications of these findings is that, when it comes to cell design, relations between neighboring beta cells are critical. It is communication between cells that creates the tent-like shape in the first place: Beta cells that are cut off from the others soon lose their edges. And if the “tent poles” help facilitate communication, then the protrusions along their length are likely to play a role in passing messages back and forth, possibly by helping align the membranes’ pores, which are just big enough to admit the calcium ions. “These findings suggest a mechanism for beta cells to function in unison,” says Shilo. “Coordinating their actions might help prevent random responses by single cells.”

Although the work was done on mouse pancreatic cells, there is already some evidence that human beta cells also have edges. These findings, says Shilo, shed light on the ways that insulin-producing beta cells function, and they could lead to new ways of thinking about the normal complex, coordinated activity of these cells, which play such a central role in our health.
 
Prof. Ben- Zion Shilo's research is supported by the M.D. Moross Institute for Cancer Research; the Carolito Stiftung; and the Mary Ralph Designated Philanthropic Fund. Prof. Shilo is the incumbent of the Hilda and Cecil Lewis Professorial Chair of Molecular Genetics.

 
 
Mouse islet of Langerhans; insulin-containing vesicles within beta cells are shown in white
Life Sciences
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Use It or Lose It

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muscle
         A 3-D computer model of a fruit fly muscle fiber with multiple nuclei

 

Everyone knows that exercise can build muscle; without exercise, muscles quickly lose their strength and volume. These facts have been common knowledge for so long, it might come as a surprise to find that very little is known about the molecular mechanisms behind them. How indeed does physical activity cause muscles to strengthen?
Talila Volk
Prof. Talila Volk
Weizmann Institute scientists have now proposed an explanation. Research conducted by the team of Prof. Talila Volk in the Molecular Genetics Department suggests that the long, cylinder-shaped muscle cells – the muscle fibers – contain proteins that function as biological “mechanosensors.” These spring-like, elastic proteins are connected to the cellular supporting structure – the cytoskeleton – on the one side, and on the other side, to the cell’s nucleus. Muscle contractions exert mechanical pressure on the cytoskeleton, which, in turn, puts pressure on these sensor proteins, causing them to transmit a signal to the nucleus.

This signal presumably alters the internal architecture of the chromosomes within the nucleus, changing gene expression – that is, the activity of genes – in the affected portion of the DNA. As a result, certain genes become activated, prompting the release of proteins that make up the filaments responsible for the contraction of the muscle fiber. In addition to contraction, the proteins fortify existing filaments and help produce new ones, building up muscle mass.

In this manner, exercise triggers a strengthening of the muscle. But because muscle-building proteins have a high turnover, the signal for their production must be periodically repeated. If, in the absence of exercise, the muscle fails to contract for a while, the mechanosensors no longer send their signals to the nucleus, ultimately leading to a loss of muscle mass.
 
muscle fibers
Muscle fibers of a fruit fly viewed under a confocal microscope: a normal fiber has normally-shaped, properly distributed nuclei (A), whereas the nuclei of fibers with mutated MSP-300 proteins are distorted and distributed abnormally (B, C and D)

 

 
Evidence for this explanation comes from a series of studies that Volk and her team – including research students Hadas Elhanany-Tamir and Miri Shnayder, and postdoctoral fellow Dr. Shuoshuo Wang – conducted in fruit flies. As reported in the Journal of Cell Biology, the scientists have identified a fruit fly protein, called MSP-300, whose shape and mechanical properties make it perfectly suited to serving as a mechanosensor. MSP-300 forms a ring around the nucleus, with numerous radial extensions connected to the cytoskeleton. It has elastic properties, as would be required from a mechanosensor; but on the other hand, it operates in close cooperation with two other proteins that help create rigid scaffolding around the nucleus, protecting it from muscle contractions. By introducing mutations into MSP-300, the scientists showed that it is indeed essential for maintaining muscle mass. The effect of the mutations on the fly’s muscles was devastating: The muscles fibers thinned out and their nuclei were deformed and clumped together abnormally. As a result, the muscles didn’t work properly, so the larvae couldn’t crawl and adult flies couldn’t fly.
 
mechanosensor protein
The MSP-300 protein, viewed here under a confocal microscope, forms a ring (red in the left image, green on the right) around the muscle cell nucleus, with extensions to the cytoskeleton

 

 
Because human muscle cells contain proteins equivalent to MSP-300, suggesting they may also function as mechanosensors, these findings can shed new light on the connection between physical activity and a healthy build-up of muscle in humans. A better understanding of this connection may in the future lead to improved ways to prevent muscle loss resulting from aging, forced inactivity as in paralysis, or such disorders as muscular dystrophy.
 
Prof. Talila Volk's research is supported by Erica A. Drake and Robert Drake. Prof. Volk is the incumbent of the Sir Ernst B. Chain Professorial Chair.
 
Life Sciences
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“Big Eaters” Get a Makeover

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When in the 1880s Russian zoologist Ilya Mechnikov first described large, voracious cells that devour bacteria and cellular debris – findings for which he later received a Nobel Prize – he called them macrophages, or “big eaters.”  Although macrophages have since been assigned numerous additional responsibilities, both in immunity and in tissue maintenance, it is the “big-eater” label that has stuck for nearly 130 years.  But recent research at the Weizmann Institute, which recently appeared in Cell, is putting a new face on the macrophage. In fact, not only one face but many: These studies show that macrophages take on different functions and appearances depending on which tissue they call home.  Prof. Steffen Jung of the Immunology Department says: “If we can learn the tricks they use to change their functions, we might be able to harness their activities to control disease.”

In the gut: Macrophages visualised as green cells in reporter mice
 
The tasks that the macrophages carry out in the various organs can be highly specific. In the nervous system, for example, they play a role in shaping nerve cells, while in the spleen they dine on well-aged red blood cells. Jung, who has been studying macrophages for a decade, recently revealed that, unlike most immune cells, many macrophages are long-lived cells that arise in the embryo, developing alongside their host organs. These findings raised new questions about macrophage development. For example, how do they get trained to serve each particular organ and tissue?

To begin to answer these questions, Jung joined up with departmental colleague Dr. Ido Amit, who investigates how regulatory regions in the genome control immunity. There are only a handful of macrophages in any one organ, but Amit and his team have developed cutting-edge techniques, including advanced robotics and next-generation sequencing technologies, to study such rare, specialized cells in their natural state. The scientists profiled these cells down to the molecular level, using the data to explain the unique ways their genes are expressed and regulated.
 
(l-r) Prof. Steffen Jung, Dr. Deborah Winter, Dr. Ido Amit and Dr. Ronnie Blecher-Gonen
 

 

        
 
The team, which also included Dr. Deborah Winter, Dr. Ronnie Blecher-Gonen, Eyal David and Dr. Hadas Keren-Shaul, all of the Weizmann Institute’s Immunology Department, and Yonit Lavin and Prof. Miriam Merad of the Icahn School of Medicine at Mount Sinai, New York, examined macrophages in seven different organs – from brain to lungs to intestines. They succeeded in identifying a unique signature for each of these populations, based on their genomic profiles and regulatory landscapes – a sort of textured map of their convoluted genetic activities. In particular, the team noted that each macrophage population used a distinct set of regulatory elements, or “enhancers,” for turning “on” or “off” the expression of certain genes.

Next the researchers switched these cells between organs. To their surprise, the macrophages began to change their signatures, taking on new profiles to fit their new surroundings. When the cells grew from immature cells, the revamping process was nearly complete – over 90%. But even when the experiment was repeated with fully differentiated cells, there were substantial changes in the macrophages’ personality profiles. Specifically, macrophages that were moved from the peritoneum to the lungs started to look and act like functional lung macrophages.
 
 
Macrophages in the brain shown in green
 
These findings, Amit and Jung believe, could change quite a few preconceived notions about macrophages. For one, these cells turn out to be incredibly plastic: “It’s a sort of ‘nature versus nurture’ issue,” says Winter, who led the study together with Blecher-Gonen. “Our findings suggest that nurture plays a much stronger role in shaping these cells’ identities than anyone had thought.” And the ways that the cells take their cues from their surroundings support Jung’s earlier findings: Macrophages arise from common precursor cells in the embryo and specialize after receiving signals from their host tissue, thus becoming an integral part of their surroundings. This goes beyond mere genetics, say the researchers: Understanding how the fate of such cells as macrophages is determined could help decipher the molecular mechanisms of diseases, including immunological disorders, anemia, leukemia and more.
 
The study was conducted in mice, but the ultimate goal is to apply the findings to humans. “In the future,” says Blecher-Gonen, “we want to learn how to retrain the macrophages ourselves. Then we could use them to treat diseases in which the patient’s macrophages are faulty or inadequate.” As an example, the team envisions creating lung macrophages that could clean up the thick secretions blocking the lungs of cystic fibrosis patients, or designer gut macrophages that could be used to treat irritable bowel disease. Amit: “Since most disease-causing mutations are located in regulatory regions, further studies could shed new light on the pathways involved in such diseases as inflammatory bowel disease and multiple sclerosis, and perhaps lead to the more precise treatment of patients.”
 
 
 
 
Ido Amit's research is supported by the M.D. Moross Institute for Cancer Research; the J&R Center for Scientific Research; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Abramson Family Center for Young Scientists; the Wolfson Family Charitable Trust; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Leona M. and Harry B. Helmsley Charitable Trust; Sam Revusky, Canada; the Florence Blau, Morris Blau and Rose Peterson Fund; the estate of Ernst and Anni Deutsch; the estate of Irwin Mandel; and the estate of David Levinson. Dr. Amit is the incumbent of the Alan and Laraine Fischer Career Development Chair.
 
Prof. Steffen Jung's research is supported by the Leir Charitable Foundations; the Leona M. and Harry B. Helmsley Charitable Trust; the Maurice and Vivienne Wohl Biology Endowment; the Adelis Foundation; Lord David Alliance, CBE; the Wolfson Family Charitable Trust; the estate of Olga Klein Astrachan; and the European Research Council.


 
 
Macrophages in the brain shown in green
Life Sciences
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Sending a Mixed Message

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In Alice in Wonderland, one side of the mushroom made her shrink, while the other side of the same mushroom made her grow. Alice may have been confused by this, but a similar paradox is often evident in biology: The same molecule can have completely opposite effects on the cells that receive its signals. These signaling molecules are secreted and consumed by cells in order to communicate with each other and coordinate actions. Thus, for example, a certain molecule can signal enhanced cell division to increase cell numbers and, at the same time, enhance the probability of cell death. Is there a reason why nature chose this counterintuitive strategy? Can one molecule somehow do both jobs better than two?
 
Paradox
 
The communication between T cells – part of the immune system’s protection against invading pathogens – provides a good basis for gleaning insight: T cells secrete a signaling molecule, called IL-2, which has the split function of increasing T-cell proliferation and inducing T-cell death. In previous collaborative research, the groups of Dr. Nir Friedman of the Weizmann Institute’s Immunology Department and Prof. Uri Alon of the Molecular Cell Biology Department had developed a mathematical model predicting that the paradoxical mechanism of IL-2 enables the body to reach a state of homeostasis – that is, maintaining a relatively steady number of cells. “Balance in such a system is important in order to prevent too large a response on the one hand, which could prove wasteful or harmful, or too weak a response on the other hand,” says Friedman.

The scientists recently joined forces again to put their theoretical predictions to the experimental test. Dr. Shlomit Reich-Zeliger and former postdoctoral fellow Dr. Yaron Antebi in Friedman’s lab, together with then PhD student Yuval Hart in Alon’s group, cultured T cells in groups of different starting sizes and followed their numbers for a week. Their findings, recently published in Cell, support the notion that T cells do indeed reach homeostasis as a result of the paradoxical IL-2  signaling – maintaining an almost fixed number of cells regardless of their initial concentration. However, again as predicted, this is only true above an initial threshold level of cell numbers. Below that threshold, the T-cell population shrinks to extinction. Friedman: “This function might serve as a kind of ‘safety switch,’ possibly to prevent an exaggerated response to a harmless trigger mistakenly identified by just a few cells.”
Prof. Uri Alon
 
The experiments helped validate further predictions: The body’s homeostasis is dependent on IL-2; T cells “lose their balance” if they can’t produce this molecule. The researchers also confirmed that IL-2 levels rise and fall, with peak levels occurring, counterintuitively, at relatively low cell numbers – just above the threshold. At this level, the higher signal probably functions to boost T-cell proliferation. 
 
Still, why use a “two-in-one” molecule? To answer the question, the scientists decided to test other possible scenarios by plugging a two-molecule solution into their mathematical model. The results showed that two separate molecules, each with its own function, would make the system more sensitive to environmental perturbations that could throw it completely off balance. In contrast, having one molecule with two functions proved to be a more robust setup, enabling the system to better sense and compensate for additional signals in the surrounding environment – something like Alice eating bits from alternate sides of the mushroom until her senses told her she had reached the right height.
Dr. Nir Friedman
 
IL-2 is used to treat various diseases, but its use is hampered by possible serious side effects. A better understanding of its complex mechanism of action may therefore help toward designing more effective interventions in the future. More generally, these findings can also be applied to other biological systems whose molecules display similarly paradoxical signaling – for example glucose, which has contradictory effects on the insulin-producing cells in the pancreas.  

This study provides an important step toward gaining a better, more quantitative understanding of the complex intercellular responses between communicating cells. By modeling the population dynamics of cells in such complex systems as the human immune system, studies like this can reveal the paradoxical nature of our existence.

Also participating in the research were Dr. Irina Zaretsky of the Immunology Department and Dr. Avraham Mayo of the Molecular Cell Biology Department.
 
Prof. Uri Alon’s research is supported by the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Braginsky Center for the Interface Between Science and Humanities; and the European Research Council. Prof. Alon is the incumbent of the Abisch-Frenkel Professorial Chair.

Dr. Nir Friedman’s research is supported by the Nella and Leon Benoziyo Center for Neurological Diseases; the Clore Center for Biological Physics; the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics; the Victor Pastor Fund for Cellular Disease Research; the Abraham and Sonia Rochlin Foundation; the Adelis Foundation; the Norman E. Alexander Family Foundation; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Crown Endowment Fund for Immunological Research; the estate of John Hunter; and the estate of Suzy Knoll. Dr. Friedman is the incumbent of the Pauline Recanati Career Development Chair.
 
 

 

 
Paradox Alice in Wonderland
Life Sciences
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How Cells Feel the Stretch

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Top right: Before force is applied, cells grown in culture are randomly oriented. Top left: As a result of cyclic stretching, the cells organize in a uniform orientation. Bottom left: Following the cyclic stretching, cell skeletal fibers (“compressed springs,” red) align at the same angle as the cell body. Bottom right: Focal adhesions (green) at the ends of cellular skeleton fibers (red)

 
As our blood vessels pulsate with each heartbeat or our lungs inflate, the cells in these vessels and organs stretch as well. Such cells, which sense rhythmic fluctuations in force, have been found to neatly align at a very uniform angle. But how do they know in which direction to orient themselves? A new look at this process suggests that dozens of tiny individual adhesion sites at the cell’s outer edges collectively “steer” the entire cell so that it points in the right direction. These findings were recently published in Nature Communications.  
   
Observations in the last decade or two have revealed that cells can sense and respond to mechanical perturbations. When cells are repeatedly stretched together with an underlying substrate to which they adhere, they tend to align – more or less – in the direction they are stretched the least. For Dr. Ariel Livne in the lab of Prof. Benjamin Geiger in the Molecular Cell Biology Department, it was this “more or less” that was problematic. The researchers realized that something was missing from the models used to predict how a cell will behave when exposed to cyclic forces.
 
Cells that are being stretched may still hold on to the underlying surface through focal adhesions – “sticky” contact points around their edges. Running between the focal adhesions is a network of cellular skeleton fibers that effectively behave as “compressed springs.” Existing models for cell reorientation under cyclic stretching focused primarily on these springs, assuming they were the driving element behind a cell’s change of direction.
(l-r) Dr. Ariel Livne, Prof. Benjamin Geiger and Dr. Eran Bouchbiner
 
But Livne’s precise experiments and analysis showed that stretching the individual springs could not account for the observed cell orientations. In collaboration with Dr. Eran Bouchbinder of the Chemical Physics Department, a theoretician who studies the physics of complex systems, including the physical behavior of surfaces that experience forces, the team developed a theory to describe the responses of focal adhesions to alternating forces. This theory was highly successful at predicting not only the new direction in which cells realign, but also the rate of the entire rotation process. Thus the reorientation of the entire cell appears to begin at the “grass roots” through individual changes in the contact points at the cell edges. 
 
Prof. Benjamin Geiger’s research is supported by the Leona M. and Harry B. Helmsley Charitable Trust; the Adelis Foundation; the Fondazione Henry Krenter; Paul and Tina Gardner, Austin, TX; David and Molly Bloom, Canada; the estate of Anne S. Lubliner; the estate of Raymond Lapon; the estate of Alice Schwarz-Gardos; and the European Research Council. Prof Geiger is the incumbent of the Professor Erwin Neter Professorial Chair of Cell and Tumor Biology.
 
(l-r) Dr. Ariel Livne, Prof. Benjamin Geiger and Dr. Eran Bouchbiner
Life Sciences
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Where Have all the Mitochondria Gone?

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It’s common knowledge that all organisms inherit their mitochondria – the cell’s “power plants” – from their mothers. But what happens to all the father’s mitochondria? Surprisingly, how – and why – paternal mitochondria are prevented from getting passed on to their offspring after fertilization is still shrouded in mystery; the only thing that’s certain is that there must be a compelling reason, seeing as this phenomenon has been conserved throughout evolution.


Now, Dr. Eli Arama and a team in the Weizmann Institute’s Molecular Genetics Department have discovered special cellular vesicles that originate in the female fruit flies’ egg and which actively seek out and destroy the father’s mitochondria upon fertilization.  

This study, recently published in Development Cell, may help shed light on the prevailing theories. One holds that it is an active process in which paternal mitochondria are selectively degraded by a “self-eating” system known as autophagy, in which vesicles called autophagosomes engulf the cell’s unwanted structures. But the autophagy study was conducted on worms (C. elegans) whose sperm are quite different from the long, flagellated “head” and “tail” structures of both mammalian and fruit-fly sperm. The tail comprises the mitochondria: a long tube attached to, or coiled around, the tail’s skeletal structure. How would the tiny autophagosome engulf such a large structure – about 2 mm long in the fruit fly?

A second theory, based mainly on mouse models, states that the absence of paternal mitochondria is due to a passive process of dilution in the sea of maternal mitochondria. But that could not explain why certain genetic markers related to autophagy were still detected on the paternal mitochondria after fertilization.

Enter the egg’s special cellular vesicles. The Weizmann team, led by Ph.D. students Liron Gal and Yoav Politi in Arama’s group, together with former senior intern Yossi Kalifa and former Ph.D. student Liat Ravid, and with the assistance of Prof. Zvulun Elazar of the Biological Chemistry Department, found that as soon as the sperm enters the egg, the cellular vesicles – already present in the fruit fly egg – immediately attract to the sperm like a magnet. They then proceed to disintegrate the sperm’s outer membrane and separate the mitochondria from the tail section, which is subsequently cut into smaller pieces that are then “devoured” by conventional selective autophagy.

But what were these vesicles? Close observation revealed they did not resemble an autophagosome, but rather a different type of vesicle that is usually involved in a distinct pathway. Yet these vesicles carried autophagy markers.  Arama: “We were not witnessing classic autophagy machinery; these structures were too large and morphologically distinct to be typical autophagosomes.”

The team’s findings suggest that the egg’s special cellular vesicles represent a new type of system that is a unique combination of three separate biological processes whose pathways may have diverged from their classic functions.

These new discoveries, which the scientists believe hold true for other organisms with flagellated sperm, including humans, may lead, among other things, toward an understanding of why only a quarter of IVF pregnancies carry to term. It may be that this invasive procedure somehow abrogates the ability of the egg to destroy the paternal mitochondria. Arama and team hope that further research will help shed new light on a variety of issues pertaining to paternal mitochondria, with an ultimate goal of understanding mitochondrial turnover and male fertility.

 

Dr. Eli Arama’s research is supported by the Yeda-Sela Center for Basic Research, the Fritz Thyssen Stiftung; and the late Rudolfine Steindling. Dr. Arama is the incumbent of the Corinne S. Koshland Career Development Chair in Perpetuity.

Life Sciences
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Gaining Potential

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(l-r) Prof. Dov Zipori, Drs. Dena Leshkowitz, Orly Ravid and Meirav Pevsner-Fischer. (Insets,l-r) Hassan Massalha and Dr. Ofer Shoshani

 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
Stem cells, we know, are highly variable. In the embryo, these cells are capable of giving rise to all the types of mature functional cells in the body; the more limited types of adult stem cell each give rise to a variety of specialized, mature cells belonging to specific tissues. But for all these stem cells the common view is somewhat uniform: It is generally believed that differentiation – the process by which the cells gain their specialization – is strictly a one-way street with signposts at every intersection. Weizmann Institute Prof. Dov Zipori has been challenging that dogma, and his recent research suggests that much of what scientists believe about stem cell activity could be mistaken.

In his lab in the Molecular Cell Biology Department, Zipori researches cells known as mesenchymal stem cells. As opposed to other types of adult stem cell, which are found in such specific locations as the bone marrow, mesenchymal cells are scattered throughout the body. Mesenchymal stem cells are usually defined by their capacity to give rise to three types of cell: bone, cartilage and fat – a sort of "golden triangle." In the basic one-way scenario, a mesenchymal stem cell divides either symmetrically, giving rise to two identical stem cells, or asymmetrically, when one daughter cell remains a stem cell and the other begins the process of differentiation. Over several rounds of division, subsequent generations of cells continue to differentiate until the specialized adult cells appear. The intermediate cells progress by shedding their differentiation potential: In each round they are increasingly limited in the kinds of tissue their progeny can become.  
 
 
Sequential appearance and disappearance of differentiation potencies, absent in the parent cell population due to single cell cloning. Left hand side is a schematic representation of the actual images of adipogenic differentiation potential seen, on the right, in reddish cells stained for fat accumulation

 
This model – including the "golden triangle" – was mostly set in stone by a scientific paper published in 1999. Mesenchymal stem cells were placed atop the triangle, as they could give rise to any of the three tissue types. Much subsequent research into these cells – and stem cells in general – has relied on this scenario. But Zipori, even then, wondered if these findings truly reflected what happens in the body. For one thing, even though it had not been shown in mammals, fruit fly experiments had found evidence that certain maturing cells in the reproductive system can revert to a stem cell state. And his own experiments with these cells suggested that mesenchymal cells were a bit more unruly than the rigid, one-way model would suggest. He had already noted in the mid-1980s that when the conditions in the cells' environment were slightly changed, some differentiated cells readily lost their mature cell properties and returned to a seemingly undifferentiated state.

By 2004, in an article he published in Nature Reviews Genetics, Zipori suggested that researchers begin to think in terms of a "stem state" – a state of the cell – rather than stem cells – an either-or category. Stemness thus implies a fluid condition that a cell might pass into or out of. He also raised the notion that this activity might happen spontaneously in the body. In fact, he wrote, the production of new stem cells could result from maturing cells gaining stem cell potential, rather than from symmetrical stem cell division.
 
stem state infographic
 
Just two years later, in 2006, the idea of the “stem state” or “stemness” was vindicated when researchers in Japan took mature cells and endowed them with stemness by reverting them back to the very first cell type – embryonic-like stem cells. This was done by artificially imposing specific gene expression in the cells. Nevertheless, few were ready to believe that cells could revert spontaneously in the body from maturity to stemness.

In the present study, which appeared recently in Stem Cell, Zipori and his team, set out to test the true rigidity of the mesenchymal differentiation pathways: Did the commonly accepted paths, with their inflexible chain of events, reflect reality? Following the procedure used in the earlier experiments, the team isolated single mesenchymal cells from mice, cloned them and grew them in lab dishes. But, using modern methods of single cell tracking and analysis, they were able to dig deeper. The study had been initiated five years earlier by Dr. Ofer Shoshani, then a Ph.D. student, who was later joined by additional members of the team, including Dr. Orly Ravid, Hassan Massalha, Alla Aharonov and Yossi Ovadya, and Drs. Meirav Pevsner-Fischer and Dena Leshkowitz of the Institute’s Bioinformatics Unit.
 
 
The researchers managed to capture mesenchymal cells in the intermediate stages of differentiation. If the original model was correct, each generation should show a progressive loss of differentiation potential. But what they found was very different: Some cells, indeed, lost a particular sort of differentiation potential – say, the ability to turn into cartilage; but others of their siblings and cousins at each stage regained it. Rather than a linear, one-way street, they now had a more jumbled picture in which cells could go back and forth from  one state to another. Although the team was looking at the potential to turn into one of the golden triangle tissues – fat, bone or cartilage – they also saw signs that the mesenchymal cells could give rise to other kinds, for example, endothelial-like or epithelial-like cells.
Mesenchymal stem cells (MSCs) seeded densely and sparsely. Left column: phase contrast images; right column: staining with antibodies to either epithelial (E-cahedrin) or endothelial (vWF) markers. (Top) Dense seeding: The cells exhibit random morphology and are negative for the two markers. (Middle) Cells grown from isolated colonies: These develop “cuboidal” shapes typical of epithelial cells and are positive for E-cahedrin. (Bottom) Other sparsely-seeded cells take on elongated shapes and are positive for vWF, the endothelial marker
 
According to Zipori, these mesenchymal cells may have easily acquired and discarded various states of stemness because they were under stress – in this case the stress of the cell being removed from the surroundings in which it normally functions and placed in a lab dish. This fits in with another observation the team had made: The cells tended to revert much less often when they were grown in low oxygen conditions. Within the body, low oxygen is the default situation for stem cells; high oxygen, in the case of injury, for example, signals stress. To Zipori, these findings hint that the body’s mesenchymal cells may jump back to higher-potential states in such situations as tissue damage, in which many types of new cells may be quickly needed.
 
Zipori: "Our findings imply that the single-cell cloning used in the past to define mesenchymal stemness may not have discovered true mesenchymal stem cells that give rise to all the differentiated types. Rather, they most likely observed intermediate mesenchymal cells that, because they were removed from their normal environment and thus grown in stressful conditions, had simply jumped back to a higher differentiation potential. Much research has relied on this model over the past 15 years; but our findings suggest that we need to rethink even our most basic assumptions about the ways that cells are renewed in our bodies."
 
Prof. Dov Zipori’s research is supported by the Helen and Martin Kimmel Institute for Stem Cell Research, which he heads; the J & R Center for Scientific Research; the Leona M. and Harry B. Helmsley Charitable Trust; David and Molly Bloom, Canada; and Roberto and Renata Ruhman, Brazil. Prof. Zipori is the incumbent of the Joe and Celia Weinstein Professorial Chair.

 

 
 
stem state infographic
Life Sciences
English

Cells Are Individuals Too

English
(l-r) Prof. Amos Tanay and Dr. Ido Amit
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Stereotyping groups of people according to the behaviors and characteristics of a few may not accurately reflect reality – it ignores diversity within these groups. Could this also be true for cells? Traditionally, cells have been classified according to type depending on their looks (round, pointed, etc.) and broad functional characteristics – for example, the immune system’s T and dendritic cells. But new research from the Weizmann Institute suggests that such generalization of cells may be misleading; rather, cells should be judged on their individual merit. “A cell has the potential to independently change its behavior by switching genes ‘on and off’ in response to various developmental signals and cues it receives from its environment. We therefore need a way to distinguish their individual characteristics and function,” says Dr. Ido Amit of the Immunology Department. 
Brain cells
 
This is easier said than done. The average biological tissue contains billions of cells, comprising hundreds – if not thousands – of different “types.” How to sample each individual? A relatively new tool holds promise: single-cell sequencing. This method sequences the DNA and RNA of single cells, allowing scientists to trace and characterize their unique individual behavior – without cell-stereotype prejudices.
Muscle cells
 
It can reveal which genes are being expressed, at what levels; whether proteins are being made, and under what conditions. This information will ultimately lead to a better understanding of how the cells work together to ensure the healthy functioning – or, in cases of disease, the malfunctioning – of tissues. 
 
But single-cell sequencing is still in its infancy and scientists have so far been able to sequence the genetic material in only a small quantity of cells from tissue cultures consisting of one “type.” Now, as reported in Science, Amit, Prof. Amos Tanay of the Computer Science and Applied Mathematics, and Biological Regulation Departments, and their teams, led by Dr. Diego Jaitin, Dr.Hadas Keren-Shaul and PhD student Ephraim Kenigsberg, together with Prof. Steffen Jung’s laboratory in the Immunology Department, have developed a new single-cell sequencing method that is able to automatically sequence and analyze the RNA from thousands of single cells at once from living samples of complex tissues.
 
To test the robustness of their new technique, the scientists sampled mouse spleen – an immune system organ whose cells are very well described – to see whether they could reverse engineer and correctly identify its cellular composition. After computationally dividing the cells into groups expressing similar genes, they ended up with seven “types” of cells in total. Some of these groups were comparable to those already described, including B cells, natural killer cells, macrophages, monocytes and dendritic cells. But to their surprise, they discovered new subpopulations of dendritic cells, with diverse functions that have, until now, gone unrecognized.
Red blood cells
 
“The use of traditional methods can be likened to observing a football game from afar,” says Tanay. “All players in a team seem identical, both in terms of outward appearance and behavior, and, for the most part, they all seem to ‘hang around’ in the same spot in the middle of the pitch. Single-cell sequencing, however, allows you to ‘zoom in’ on the action and distinguish the unique position and role of each player within the team – defense, attack, goalkeeper.”
 
In a follow-up experiment intended to simulate an immune response, the scientists exposed mice to a substance that mimics infection in order to test whether their method is able to correctly identify immune cells “in action.”
 
In response to changes in environmental cues, the same “types” of immune cells were identified, but the relative proportion of each changed, as did the genes expressed and the amount of RNA produced within each cell, both within and between cell groups. “Taken together, these findings paint a more complex picture of cell identity, suggesting that ultimately, defining cells according to ‘type’ is somewhat irrelevant and we should be letting individual cells ‘speak for themselves’,” says Kenigsberg.
Skin cells
 
This is just the beginning. Jaitin: “Single-cell RNA sequencing has huge potential in answering as yet unsolvable questions in biology, as well as having clinical implications in areas ranging from immune disorders to neurodegeneration, metabolism, stem cells and cancer. For example, we could apply these new tools to discover exactly which tumor cells are resistant to therapy.”

“The experimental protocol and analysis algorithms we developed make single-cell RNA sequencing of thousands of cells efficient, reliable and affordable,” says Keren-Shaul. Indeed, achieving a throughput about 30 times higher than current techniques, the team believes that the single-cell characterization of complex tissues is poised to increase the amount of detail able to be ascertained and bring new insights into multiple fields in biology and medicine.
 
Dr. Ido Amit's research is supported by M.D. Moross Institute for Cancer Research; the Abramson Family Center for Young Scientists; the Wolfson Family Charitable Trust; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Leona M. and Harry B. Helmsley Charitable Trust; Sam Revusky, Canada; Drs. Herbert and Esther Hecht, Beverly Hills, CA; the estate of Ernst and Anni Deutsch; and the Estate of Irwin Mandel. Dr. Amit is the incumbent of the Alan and Laraine Fischer Career Development Chair.
 
Prof. Steffen Jung's research is supported by the Leir Charitable Foundations; the Leona M. and Harry B. Helmsley Charitable Trust; the Maurice and Vivienne Wohl Biology Endowment; the Adelis Foundation; Lord David Alliance, CBE; the Wolfson Family Charitable Trust; the estate of Olga Klein Astrachan; and the European Research Council.
 
Prof.  Amos Tanay's research is supported by the Helen and Martin Kimmel Award for Innovative Investigation; Pascal and Ilana Mantoux, Israel/France; the Wolfson Family Charitable Trust; the Rachel and Shaul Peles Fund for Hormone Research; and the estate of Evelyn Wellner.


 
All cell images: Thinkstock
 
 

 

 

 

 
 
(l-r) Prof. Amos Tanay and Dr. Ido Amit
Life Sciences
English

The Collagen Paradox

English
 
 
Lital Bentovim and Prof. Elazar Zelzer
 
Without collagen, we would all go to pieces – quite literally. This large molecule, the most abundant protein in our bodies, is the “glue” that holds tissues together. In fact, in our distant evolutionary past, it was collagen that enabled our single-celled ancestors to evolve into multi-celled creatures – by helping individual cells stick together.

During embryonic development, large amounts of collagen – the starting material for bone formation – are produced in the growing bone. Since collagen production is a complex, multi-stage process that requires a great deal of oxygen, one would expect to see a massive supply of oxygen to this developing body part.
 
Yet paradoxically, the growing bone is exceptionally low in oxygen: As an internal organ, it receives less oxygen than external embryonic tissues. In fact, oxygen-carrying blood vessels are actively pushed out of the cartilage that builds up in preparation for bone formation.  
 
Cartilage cells in the growth plate of a developing bone. When the expression of the Hif1a gene is blocked, the number of cells in the growth plate’s low-oxygen zone is reduced and their supporting matrix is diminished (right)
 

 

 
 
 
 
 
 
 
 
A study conducted at the Weizmann Institute of Science and published in Development sheds light on this paradox. Though it remains unknown why so little oxygen is available during bone formation, the Weizmann findings explain how collagen production can take place in such seemingly unfavorable conditions.

Prof. Elazar Zelzer, Lital Bentovim and then grauate student Dr. Roy Amarilio, all of the Molecular Genetics Department, investigated collagen formation in the growing bones of mouse embryos, focusing on a molecule, HIF1-alpha, which is known to regulate the cellular and physiological responses to low-oxygen conditions in tissues. The scientists discovered that HIF1-alpha also serves as a central regulator of collagen formation and renders the process highly efficient, so as to make the most of the available oxygen. When they blocked the action of this molecule, collagen release was impaired and the bone did not grow properly.
 
Cartilage cells that secrete collagen (red) under low-oxygen conditions, viewed under a fluorescent microscope (left). When the Hif1a gene is knocked out, collagen is not secreted properly (right)
 

 

 
The scientists found that like a capable manager, HIF1-alpha creates optimal conditions for the collagen production. First it increases the release of catalytic enzymes that speed up the process. Then it shuts down other metabolic processes in the tissue, so that the little oxygen available can be channeled in its entirety to the collagen-secreting cells, enabling them to focus exclusively on their main task.

In addition to clarifying the formation in the embryo of one of the body’s central building blocks, this study may contribute to our understanding of disease. It may, for example, help explain how certain cancers develop despite low oxygen levels in the malignant tissue.
 

Attached

Dr. Einat Blitz
 
Bones, muscles and tendons give the body form, keep it stable and enable it to move. But for these functions to be successfully performed, they must be assembled into a single, precisely regulated system – the musculoskeletal system. A another study conducted in Zelzer's lab, reported in Development, has revealed a crucial mechanism responsible for this assembly.

A fundamental step in the assembly process is the development of attachment units between a bone and a tendon – protrusions of various shapes and sizes known in technical language as bone eminences, which grow on the surface of the bone. These protrusions are vital for the proper functioning of the musculoskeletal system: They provide stable anchoring points for muscles that are inserted into the bone via tendons, as well as helping dissipate the stress exerted on the bone by contracting muscles.
 
Developing bone in normal (top) and mutant (bottom) embryos. Protrusions in a developing bone are formed by a distinct class of cells (green) that differ from the regular bone-forming cells (yellow-orange). Incorrect regulation and distribution of these cells leads to irregularities in the shape of the forming bone

 

 

 
 
In the new study, conducted in mouse embryos, the scientists have discovered that the bone protrusions are formed by a distinct, previously unknown class of cells that differ from the regular bone-forming cells. These protrusion-forming cells have a split personality of sorts: They are controlled simultaneously by two genetic programs – one characteristic of bone, the other of ligaments and tendons. This dual nature is what facilitates the attachment of the tendons, ligaments and muscles to the bone protrusions.

The scientists were able to establish the details of the genetic programs, including the molecular signaling that regulates them, by creating mutant mouse embryos lacking certain genes and tracing the embryonic development. The research was performed by Zelzer and then graduate student Dr. Einat Blitz.
A modular model: two distinct classes of cells – forming cartilage (orange) and attachment units (green) – take part in bone development

 
 
 
By revealing that bones are created in the embryo in a modular fashion, the study might help explain their mechanical properties – for example, the ability of different anatomic regions of bone to cope differently with stress and load, and their contribution to the skeleton’s overall sturdiness and flexibility.
 
Dr. Elazar Zelzer’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Helen and Martin Kimmel Institute for Stem Cell Research; the Irving and Dorothy Rom Charitable Trust and the estate of David Levinson.  
 
 

 

 

 

 

 
 

 

 
 
 
 
Developing bone in normal (top) and mutant (bottom) embryos. Protrusions in a developing bone are formed by a distinct class of cells (green) that differ from the regular bone-forming cells (yellow-orange). Incorrect regulation and distribution of these cells leads to irregularities in the shape of the forming bone
Life Sciences
English

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